/*
* Class: hdf_hdf5lib_H5
* Method: H5Aget_info
* Signature: (J)Lhdf/hdf5lib/structs/H5A_info_t;
*/
JNIEXPORT jobject JNICALL
Java_hdf_hdf5lib_H5_H5Aget_1info
(JNIEnv *env, jclass clss, jlong attr_id)
{
herr_t status = -1;
H5A_info_t ainfo;
jvalue args[4];
jobject ret_obj = NULL;
status = H5Aget_info((hid_t)attr_id, &ainfo);
if (status < 0) {
h5libraryError(env);
} /* end if */
else {
args[0].z = ainfo.corder_valid;
args[1].j = ainfo.corder;
args[2].i = ainfo.cset;
args[3].j = (jlong)ainfo.data_size;
CALL_CONSTRUCTOR("hdf/hdf5lib/structs/H5A_info_t", "(ZJIJ)V", args);
} /* end else */
return ret_obj;
} /* end Java_hdf_hdf5lib_H5_H5Aget_1info */
void pyne::Material::_load_comp_protocol1(hid_t db, std::string datapath, int row) {
std::string nucpath;
hid_t data_set = H5Dopen2(db, datapath.c_str(), H5P_DEFAULT);
hsize_t data_offset[1] = {row};
if (row < 0) {
// Handle negative row indices
hid_t data_space = H5Dget_space(data_set);
hsize_t data_dims[1];
H5Sget_simple_extent_dims(data_space, data_dims, NULL);
data_offset[0] += data_dims[0];
};
// Grab the nucpath
hid_t nuc_attr = H5Aopen(data_set, "nucpath", H5P_DEFAULT);
H5A_info_t nuc_info;
H5Aget_info(nuc_attr, &nuc_info);
hsize_t nuc_attr_len = nuc_info.data_size;
hid_t str_attr = H5Tcopy(H5T_C_S1);
H5Tset_size(str_attr, nuc_attr_len);
char * nucpathbuf = new char [nuc_attr_len];
H5Aread(nuc_attr, str_attr, nucpathbuf);
nucpath = std::string(nucpathbuf, nuc_attr_len);
delete[] nucpathbuf;
// Grab the nuclides
std::vector<int> nuclides = h5wrap::h5_array_to_cpp_vector_1d<int>(db, nucpath, H5T_NATIVE_INT);
int nuc_size = nuclides.size();
hsize_t nuc_dims[1] = {nuc_size};
// Get the data hyperslab
hid_t data_hyperslab = H5Dget_space(data_set);
hsize_t data_count[1] = {1};
H5Sselect_hyperslab(data_hyperslab, H5S_SELECT_SET, data_offset, NULL, data_count, NULL);
// Get memory space for writing
hid_t mem_space = H5Screate_simple(1, data_count, NULL);
// Get material type
size_t material_struct_size = sizeof(pyne::material_struct) + sizeof(double)*nuc_size;
hid_t desc = H5Tcreate(H5T_COMPOUND, material_struct_size);
hid_t comp_values_array_type = H5Tarray_create2(H5T_NATIVE_DOUBLE, 1, nuc_dims);
// make the data table type
H5Tinsert(desc, "mass", HOFFSET(pyne::material_struct, mass), H5T_NATIVE_DOUBLE);
H5Tinsert(desc, "density", HOFFSET(pyne::material_struct, density),
H5T_NATIVE_DOUBLE);
H5Tinsert(desc, "atoms_per_molecule", HOFFSET(pyne::material_struct, atoms_per_mol),
H5T_NATIVE_DOUBLE);
H5Tinsert(desc, "comp", HOFFSET(pyne::material_struct, comp), comp_values_array_type);
// make the data array, have to over-allocate
material_struct * mat_data = new material_struct [material_struct_size];
// Finally, get data and put in on this instance
H5Dread(data_set, desc, mem_space, data_hyperslab, H5P_DEFAULT, mat_data);
mass = (*mat_data).mass;
density = (*mat_data).density;
atoms_per_molecule = (*mat_data).atoms_per_mol;
for (int i = 0; i < nuc_size; i++)
comp[nuclides[i]] = (double) (*mat_data).comp[i];
delete[] mat_data;
H5Tclose(str_attr);
//
// Get metadata from associated dataset, if available
//
std::string attrpath = datapath + "_metadata";
bool attrpath_exists = h5wrap::path_exists(db, attrpath);
if (!attrpath_exists)
return;
hid_t metadatapace, attrtype, metadataet, metadatalab, attrmemspace;
int attrrank;
hvl_t attrdata [1];
attrtype = H5Tvlen_create(H5T_NATIVE_CHAR);
// Get the metadata from the file
metadataet = H5Dopen2(db, attrpath.c_str(), H5P_DEFAULT);
metadatalab = H5Dget_space(metadataet);
H5Sselect_hyperslab(metadatalab, H5S_SELECT_SET, data_offset, NULL, data_count, NULL);
attrmemspace = H5Screate_simple(1, data_count, NULL);
H5Dread(metadataet, attrtype, attrmemspace, metadatalab, H5P_DEFAULT, attrdata);
// convert to in-memory JSON
Json::Reader reader;
reader.parse((char *) attrdata[0].p, (char *) attrdata[0].p+attrdata[0].len, metadata, false);
// close attr data objects
H5Fflush(db, H5F_SCOPE_GLOBAL);
H5Dclose(metadataet);
H5Sclose(metadatapace);
H5Tclose(attrtype);
// Close out the HDF5 file
H5Fclose(db);
};
